SECIM is proud to host Dr. Peter Karp from SRI International for his seminar and tutorial entitled:
“Metabolic Reconstruction, Modeling, and Metabolomics Analysis in BioCyc”
Peter Karp, PhD
Director, Bioinformatics Research Group
Artificial Intelligence Center
- Date: Friday, July 8, 2016
- Time: 9:00 a.m. – 1:00 p.m.
- Location: Clinical and Translational Research Building (CTRB) Room 2161
Please circulate Dr. Karp’s Seminar Flyer to any interested parties.
Peter Karp, Ph.D., director of the Bioinformatics Research Group at SRI International, works in the interdisciplinary field of bioinformatics, which develops computer-science methods for managing and analyzing the burgeoning quantities of biological data and knowledge. Dr. Karp has been a pioneer in metabolic-pathway bioinformatics. His group has developed a metabolic-pathway database called EcoCyc that charts the complete biochemical factory within an Escherichia coli cell. His group has also developed algorithms for visualization of metabolic networks, for predicting anti-bacterial drug targets within metabolic networks, and for predicting the metabolic pathways of an organism whose genome has been sequenced. The latter algorithm has been applied to hundreds of organisms.
BioCyc.org is an extensive and user-friendly genome informatics portal containing 7,600 microbial genomes and associated metabolic pathways. This four hour tutorial will cover many aspects of BioCyc, with a focus on metabolomics data analysis. The following list is the preliminary agenda for Dr. Karp’s tutorial:
Introduction to BioCyc
o Generation of BioCyc databases
o Search operations
o Gene, metabolite, reaction, and pathway pages
o Genome browser
o BLAST search, sequence pattern search, extracting sequences
Metabolomics Data Analysis
o Metabolic network browser
o Displaying metabolomics data on individual pathways and metabolic network diagrams
o Enrichment analysis
o Pathway perturbation analysis
o Pathway collages — of customized multi-pathway diagrams overlaid with experimental data
o Using SmartTables to store, share, and analyze lists of genes and metabolites
Comparative analysis in BioCyc
o Multi-organism search
o Comparative genome browser
o Orthologs in BioCyc
o Comparison of pathway and metabolite sets
Attendees are required to register for the event. Please complete the form below to secure your spot.